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SMTL ID : 3pwk.1
Crystal Structure of Aspartate beta-Semialdehide Dehydrogenase from Streptococcus pneumoniae with 2',5'-Adenosine diphosphate and D-2-aminoadipate
Coordinates
PDB Format
Compare
Method
X-RAY DIFFRACTION 1.50 Å
Oligo State
homo-dimer
Ligands
2 x
25A
:
5'-O-MONOPHOSPHORYLADENYLYL(2'->5')ADENYLYL(2'->5')ADENOSINE
(Non-covalent)
25A.1:
15 residues within 4Å:
Chain A:
G.9
,
A.10
,
T.11
,
G.12
,
A.13
,
A.36
,
S.37
,
R.39
,
S.40
,
T.57
,
S.71
,
A.72
,
T.76
,
G.161
,
M.162
20
PLIP interactions
:
20 interactions with chain A
Hydrogen bonds:
A:G.9
,
A:T.11
,
A:T.11
,
A:T.11
,
A:G.12
,
A:A.13
,
A:S.37
,
A:S.37
,
A:S.40
,
A:S.40
,
A:M.162
Water bridges:
A:V.14
,
A:V.14
,
A:R.39
,
A:T.57
,
A:K.79
,
A:K.79
,
A:A.160
,
A:G.163
Salt bridges:
A:R.39
25A.8:
15 residues within 4Å:
Chain B:
G.9
,
A.10
,
T.11
,
G.12
,
A.13
,
A.36
,
S.37
,
R.39
,
S.40
,
T.57
,
S.71
,
A.72
,
T.76
,
G.161
,
M.162
19
PLIP interactions
:
19 interactions with chain B
Hydrogen bonds:
B:G.9
,
B:T.11
,
B:T.11
,
B:G.12
,
B:A.13
,
B:S.37
,
B:S.37
,
B:S.40
,
B:S.40
,
B:T.76
,
B:M.162
Water bridges:
B:V.14
,
B:V.14
,
B:R.39
,
B:R.39
,
B:T.57
,
B:Y.80
,
B:G.163
Salt bridges:
B:R.39
2 x
L14
:
trans-cyclohexane-1,4-dicarboxylic acid
(Non-covalent)
L14.2:
9 residues within 4Å:
Chain A:
N.94
,
S.96
,
R.99
,
N.127
,
G.159
,
A.160
,
E.220
,
K.223
,
R.245
8
PLIP interactions
:
8 interactions with chain A
Hydrophobic interactions:
A:N.127
Water bridges:
A:S.96
,
A:D.210
,
A:D.210
,
A:R.245
Salt bridges:
A:R.99
,
A:K.223
,
A:R.245
L14.9:
9 residues within 4Å:
Chain B:
N.94
,
S.96
,
R.99
,
N.127
,
G.159
,
A.160
,
E.220
,
K.223
,
R.245
7
PLIP interactions
:
7 interactions with chain B
Hydrophobic interactions:
B:N.127
Water bridges:
B:S.96
,
B:R.245
,
B:R.245
Salt bridges:
B:R.99
,
B:K.223
,
B:R.245
8 x
EDO
:
1,2-ETHANEDIOL
(Non-functional Binders)
EDO.3:
4 residues within 4Å:
Chain A:
E.24
,
S.25
,
W.332
,
E.339
2
PLIP interactions
:
2 interactions with chain A
Hydrogen bonds:
A:E.24
Water bridges:
A:E.339
EDO.4:
7 residues within 4Å:
Chain A:
Q.17
,
S.250
,
V.297
,
G.298
,
D.324
,
L.326
,
L.327
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:S.250
,
A:G.298
Water bridges:
A:Q.17
EDO.5:
4 residues within 4Å:
Chain A:
L.311
,
D.312
Chain B:
T.225
,
K.229
3
PLIP interactions
:
1 interactions with chain A
,
2 interactions with chain B
Water bridges:
A:D.312
,
B:D.235
Hydrogen bonds:
B:K.229
EDO.6:
2 residues within 4Å:
Chain A:
N.295
,
F.303
1
PLIP interactions
:
1 interactions with chain A
Hydrogen bonds:
A:N.295
EDO.10:
4 residues within 4Å:
Chain B:
E.24
,
S.25
,
W.332
,
E.339
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:E.24
Water bridges:
B:E.339
,
B:E.339
EDO.11:
7 residues within 4Å:
Chain B:
Q.17
,
S.250
,
V.297
,
G.298
,
D.324
,
L.326
,
L.327
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:S.250
,
B:G.298
EDO.12:
2 residues within 4Å:
Chain B:
N.295
,
F.303
1
PLIP interactions
:
1 interactions with chain B
Hydrogen bonds:
B:N.295
EDO.13:
4 residues within 4Å:
Chain A:
T.225
,
K.229
Chain B:
L.311
,
D.312
4
PLIP interactions
:
4 interactions with chain A
Hydrogen bonds:
A:K.229
Water bridges:
A:K.229
,
A:D.235
,
A:D.235
2 x
NA
:
SODIUM ION
(Non-functional Binders)
NA.7:
5 residues within 4Å:
Chain A:
I.273
,
A.274
,
A.275
,
F.276
,
A.279
3
PLIP interactions
:
3 interactions with chain A
Hydrogen bonds:
A:A.279
Water bridges:
A:A.274
,
A:L.281
NA.14:
2 residues within 4Å:
Chain B:
D.147
,
S.236
2
PLIP interactions
:
2 interactions with chain B
Hydrogen bonds:
B:S.236
,
B:A.238
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Pavlovsky, A.G. et al., Structural Characterization of Inhibitors with Selectivity against Members of a Homologous Enzyme Family. Chem.Biol.Drug Des. (2012)
Release Date
2012-01-04
Peptides
Aspartate-semialdehyde dehydrogenase:
A
B
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
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Aspartate-semialdehyde dehydrogenase
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2gyy.1
|
2gyy.2
|
2gz1.1
|
2gz2.1
|
2gz3.1
|
2gz3.2
|
2gz3.3
|
3pws.1
|
3pyl.1
|
3pyl.2
|
3pyx.1
|
3pzb.1
|
3q11.1
|
3q1l.1
|
3q1l.2
|
4r3n.1
|
4r3w.1
|
4r41.1
|
4r4j.1
|
4r51.1
|
4r54.1
|
4r5h.1
Cartoon
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